twodanalysis.BioPolymer2D

class twodanalysis.BioPolymer2D(obj, surf_selection=None, biopol_selection=None, start=None, step=None, end=None, by_frames=True, surf_axis='z')[source]

Class Initialization.

Parameters:

  • obj (AtomGroup or Universe) – Selection to initialize the class. If initialized with a Universe it will take the whole Universe as AtomGroup. The MDAnalysis Universe and AtomGroup will be accesible to with the self.universe and self.atom_group class attributes.

  • surf_selection (str, optional) – String selection in MDAnalysis format to define the surface (recomended). If surf_selection is given, surf_pos attribute will save the mean position of the surface over the time. This will particularly important for setting the zlim variable some of the analysis require. By default None

  • biopol_selection (str, optional) – String selection in MDAnalysis format to define the biopolymer as a selection of a Universe or AtomGroup. If None, all the AtomGroup or Universe from obj is used. Default in None.

  • start (float, optional) – Starting time or frame from the trajectory to initialize the object. If by_frames=True, it will be considered as the frame number of the trajectory to start the object. If by_frames=False, it will set the time in ns. If None, start is frame 0 of the trajectory. By default None

  • step (float, optional) – Time or frame steps from the trajectory to initialize the object. If by_frames=True, it will be considered as the step of frames of the trajectory to consider. If by_frames=False, it will set the time steps in ns. If None, all the frames of the trajectory are considered. By default None

  • end (float, optional) – Final time or frame from the trajectory to initialize the object. If by_frames=True, it will be considered as the final frame number of the trajectory to consider. If by_frames=False, it will set the time in ns. If None, end is frame 0 of the trajectory. By default None

  • by_frame (bool, optional) – Whether or not to consider ‘start’, ‘step’ and ‘end’ inputs as frame values. If False, they are consider as time values in ns.

  • surf_axis (str, optional) – Set in which distance is the surface. By default ‘z’

Raises:

TypeError – Error raised if class is not initialized with a Universe or AtomGroup

__init__(obj, surf_selection=None, biopol_selection=None, start=None, step=None, end=None, by_frames=True, surf_axis='z')[source]

Methods

FilterMinFrames(pos, zlim, Nframes[, ...])

Selects a set of Nframes in which the AtomGroup is closer to the surface and bellow a zlim threshold distance to the surface.

HbondsPerResidues([sorted, unique_res])

Computes the number of H-bonds of each residue during the simulation.

INFO()

Prints general information of the Universe and/or Atomgroup

KDEAnalysisSelection(select_res, Nframes[, ...])

KDE Contours for a set of selected residues.

ListPathsInLevel(kde_plot, contour_level[, ...])

Lists vertices of a path in a contour level of the KDE plot.

PolarAnalysis(select_res, Nframes[, zlim, ...])

Makes a Polar Histogram of the positions of the center of mass of select_res residues considering Nframes closest to the surface within the < zlim threshold.

RgPerpvsRgsPar(rgs, color[, marker, plot, ...])

Generates \(R_{g\perp}\) vs.

__delattr__(name, /)

Implement delattr(self, name).

__dir__()

Default dir() implementation.

__eq__(value, /)

Return self==value.

__format__(format_spec, /)

Default object formatter.

__ge__(value, /)

Return self>=value.

__getattribute__(name, /)

Return getattr(self, name).

__getstate__()

Helper for pickle.

__gt__(value, /)

Return self>value.

__hash__()

Return hash(self).

__init_subclass__

This method is called when a class is subclassed.

__le__(value, /)

Return self<=value.

__lt__(value, /)

Return self<value.

__ne__(value, /)

Return self!=value.

__new__(*args, **kwargs)

__reduce__()

Helper for pickle.

__reduce_ex__(protocol, /)

Helper for pickle.

__setattr__(name, value, /)

Implement setattr(self, name, value).

__sizeof__()

Size of object in memory, in bytes.

__str__()

Return str(self).

__subclasshook__

Abstract classes can override this to customize issubclass().

_recalculate_frames([triggered_by])

Recalculate frame-related attributes based on startT, endT, and stepT or startF, endF, and stepF.

computeRG2D(masses, total_mass)

Computes parallel, perpendicular and 3D radius of gyration in 1 frame.

getAreas(paths, contour_lvl[, getTotal])

Computes the area of each path a given contour level.

getCOMs([inplace, select])

Computes positions of selection from self.startT to self.endT with self.stepT steps of time.

getHbonds(selection1, selection2[, ...])

Computes H-bonds between to selection1 and selection2 of the trajectory using MDAnalysis.analysis.hydrogenbonds.HydrogenBondAnalysis.

getKDEAnalysis(zlim, Nframes[, axis, ...])

Computes KDE Contours using seaborn.kde_plot() function and extracts the paths of each contour level.

getPositions([pos_type, surf_is_zero, ...])

Computes positions of selection from self.startT to self.endT with self.stepT steps of times.

getRgs2D([plot])

Computes the radii of gyration over the trajectory using computeRG2D method.

plotHbondsPerResidues(paths_for_contour[, ...])

Makes a figure showing the center of mass of the residues with H-bonds.

plotPathsInLevel(paths, contour_lvl[, ...])

Plots the paths of a given contour level.

Attributes

__annotations__

__doc__

__module__

__weakref__

list of weak references to the object